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At some point in his life, Tom was banished to the Deeps, where he soon became a renegade. After spending years in the Deeps, the radiation mutated him into his hideous appearance. At one point he formed an alliance with the Styx, even becoming friends with the Rebeccas. He and Drake clashed many times, with the latter setting a restraining order against Tom and the other renegades.

When Drake took Will, Chester, and Cal on patrol to learn how to use the stove guns, the group encounters Cox, who frightens the young men before Drake threatens him away. He is later seen torturing a captured renegade along with several Limiters and the Rebeccas. Will and Elliott believe the renegade to be Drake and shoot him, attracting attention to Cox and the Styx, but they escape before they can give chase.

After Will's group and the Rebeccas fell down the Pore, Tom gave his condolences to the old Styx, afterwards asking for info on the Styx's plan to purge the Deeps of renegades. He participates in the search down the Pore for the Dominion phials.

After old Styx learns that the Rebeccas, Will, and Elliott survived the fall, he orders a pair of Limiters to hurl Cox into the Pore, giving him a chance to keep his end of the deal of delivering Will over to the Styx.

During the events of Closer, Tom managed to find his way to the inner world. Painfully navigating through the sunlit world, he soon reached the outskirts of New Germania, stealing food. The New Germanians captured him and presented him to the assembled Styx and New Germanian soldiers. The Rebeccas ordered his release.

He participated in the assault on the pyramid to capture Will and Dr. Burrows to recover the Dominion Phials. When the two were finally caught, Tom was in charge of interrogating Will. He began by slashing Will's stomach with a scythe, afterwards threatening to slice off Will's tongue for spitting in Rebecca One's face. The twin then announced to Elliott that Cox would cut off one of Will's fingers for every ten minutes it took for her to resopond. Before the first of Will's fingers were sliced, however, Elliott shot Tom in the head with her rifle, quickly killing him.

His body was later brought back to New Germania for a proper funeral. The Rebeccas even joked about putting a giant statue of Cox up in his honor right in front of the Chancellery.

Tom Cox was said have been very hideous in appearance, with melon sized growths on his face, black, cracked lips, and perfectly white eyes, which resemble boiled eggs. His hands were gnarled, and his body structure was
terribly deformed.